IMPPAT Phytochemical information: 
Berberine
Berberine
Summary

SMILES: COc1c(OC)ccc2c1c[n+]1CCc3c(-c1c2)cc1c(c3)OCO1
InChI: InChI=1S/C20H18NO4/c1-22-17-4-3-12-7-16-14-9-19-18(24-11-25-19)8-13(14)5-6-21(16)10-15(12)20(17)23-2/h3-4,7-10H,5-6,11H2,1-2H3/q+1
InChIKey: YBHILYKTIRIUTE-UHFFFAOYSA-N
DeepSMILES: COccOC))cccc6c[n+]CCcc-c6c%10))cccc6)OCO5
Scaffold Graph/Node/Bond level: c1ccc2c[n+]3c(cc2c1)-c1cc2c(cc1CC3)OCO2
Scaffold Graph/Node level: C1CCC2CN3CCC4CC5OCOC5CC4C3CC2C1
Scaffold Graph level: C1CCC2CC3C(CCC4CC5CCCC5CC43)CC2C1
Functional groups: cOC; c[n+](c)C; c1cOCO1
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Alkaloids and derivatives
ClassyFire Class: Protoberberine alkaloids and derivatives
Synonymous chemical names:
berberine, berbericine, umbellatine, Umbellatine
External chemical identifiers:
CID:CID_2353; ChEMBL:CHEMBL295124; ChEBI:CHEBI:16118; ZINC:ZINC000003779067; FDASRS:0I8Y3P32UF; SureChEMBL:SCHEMBL25632; MolPort-002-507-191
Chemical structure download
2D:2D MOL2D MOL22D SDF
3D:3D MOL3D MOL23D SDF3D PDB3D PDBQT
Berberine
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 336.37
Log P RDKit 3.1
Topological polar surface area (Å2) RDKit 40.8
Number of hydrogen bond acceptors RDKit 4
Number of hydrogen bond donors RDKit 0
Number of carbon atoms RDKit 20
Number of heavy atoms RDKit 25
Number of heteroatoms RDKit 5
Number of nitrogen atoms RDKit 1
Number of sulfur atoms RDKit 0
Number of chiral carbon atoms RDKit 0
Stereochemical complexity RDKit 0
Number of sp hybridized carbon atoms RDKit 0
Number of sp2 hybridized carbon atoms RDKit 15
Number of sp3 hybridized carbon atoms RDKit 5
Shape complexity RDKit 0.25
Number of rotatable bonds RDKit 2
Number of aliphatic carbocycles RDKit 0
Number of aliphatic heterocycles RDKit 2
Number of aliphatic rings RDKit 2
Number of aromatic carbocycles RDKit 2
Number of aromatic heterocycles RDKit 1
Number of aromatic rings RDKit 3
Total number of rings RDKit 5
Number of saturated carbocycles RDKit 0
Number of saturated heterocycles RDKit 0
Number of saturated rings RDKit 0
Number of Smallest Set of Smallest Rings (SSSR) RDKit 5
Berberine
Drug-likeness
Property nameToolProperty value
Number of Lipinski’s rule of 5 violations RDKit 0
Lipinski’s rule of 5 filter RDKit Passed
Number of Ghose filter violations RDKit 0
Ghose filter RDKit Passed
Veber filter RDKit Good
Pfizer 3/75 filter RDKit Bad
GSK 4/400 filter RDKit Good
Weighted quantitative estimate of drug-likeness (QEDw) score RDKit 0.674491
Berberine
ADME properties
Property nameToolProperty value
Bioavailability score SwissADME 0.55
Solubility class [ESOL] SwissADME Moderately soluble
Solubility class [Silicos-IT] SwissADME Moderately soluble
Blood Brain Barrier permeation SwissADME Yes
Gastrointestinal absorption SwissADME High
Log Kp (Skin permeation, cm/s) SwissADME -5.78
Number of PAINS structural alerts SwissADME 0
Number of Brenk structural alerts SwissADME 1
CYP1A2 inhibitor SwissADME Yes
CYP2C19 inhibitor SwissADME No
CYP2C9 inhibitor SwissADME No
CYP2D6 inhibitor SwissADME Yes
CYP3A4 inhibitor SwissADME Yes
P-glycoprotein substrate SwissADME Yes
Berberine
Phytochemical - Human target proteins supported by experimental evidence associations
Human target proteins supported by experimental evidence
IMPPAT target identifierGene identifierHGNC symbolEntrez Gene identifierSource
TAR_EXP_001140ENSG00000115592PRKAG353632ChEMBL
TAR_EXP_001058ENSG00000106617PRKAG251422ChEMBL
TAR_EXP_000905ENSG00000198712MT-CO24513ChEMBL, NPASS
TAR_EXP_000881ENSG00000087085ACHE43ChEMBL, NPASS
TAR_EXP_000880ENSG00000118058KMT2A4297NPASS
TAR_EXP_000853ENSG00000276155MAPT4137NPASS
TAR_EXP_000798ENSG00000055118KCNH23757ChEMBL, NPASS
TAR_EXP_000759ENSG00000169429CXCL83576ChEMBL
TAR_EXP_000687ENSG00000100644HIF1A3091NPASS
TAR_EXP_000411ENSG00000165092ALDH1A1216NPASS
TAR_EXP_001166ENSG00000186951PPARA5465ChEMBL
TAR_EXP_000298ENSG00000151632AKR1C21646ChEMBL, NPASS
TAR_EXP_000280ENSG00000160868CYP3A41576NPASS
TAR_EXP_000276ENSG00000272532CYP2D61565ChEMBL, NPASS
TAR_EXP_000264ENSG00000138061CYP1B11545ChEMBL, NPASS
TAR_EXP_000263ENSG00000140505CYP1A21544ChEMBL, NPASS
TAR_EXP_000132ENSG00000137491SLCO2B111309ChEMBL, NPASS
TAR_EXP_000061ENSG00000134538SLCO1B110599ChEMBL, NPASS
TAR_EXP_000004ENSG00000094631HDAC610013ChEMBL
TAR_EXP_000616ENSG00000111700SLCO1B328234ChEMBL, NPASS
TAR_EXP_001170ENSG00000112033PPARD5467ChEMBL
TAR_EXP_000450ENSG00000004487KDM1A23028ChEMBL
TAR_EXP_001194ENSG00000132356PRKAA15562ChEMBL
TAR_EXP_001914ENSG00000148344PTGES9536ChEMBL, NPASS
TAR_EXP_001810ENSG00000067955CBFB865NPASS
TAR_EXP_001807ENSG00000196139AKR1C38644ChEMBL, NPASS
TAR_EXP_001631ENSG00000165409TSHR7253ChEMBL, NPASS
TAR_EXP_001599ENSG00000164362TERT7015ChEMBL, NPASS
TAR_EXP_001547ENSG00000275349SMN16606NPASS
TAR_EXP_001343ENSG00000114200BCHE590ChEMBL, NPASS
TAR_EXP_001191ENSG00000085377PREP5550NPASS
TAR_EXP_001306ENSG00000196396PTPN15770ChEMBL, NPASS
TAR_EXP_001203ENSG00000181929PRKAG15571ChEMBL
TAR_EXP_001197ENSG00000131791PRKAB25565ChEMBL
TAR_EXP_001196ENSG00000111725PRKAB15564ChEMBL
TAR_EXP_001195ENSG00000162409PRKAA25563ChEMBL